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Merged
sphuber merged 11 commits into from
Aug 30, 2023
Merged

SIRIUS-CP2K protocol and workchain #312

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b8713d2
SIRIUS-CP2K protocol and workchain
HosseinMir Jul 12, 2023
0bd856d
Remove folder and yaml file with pseudos.
yakutovicha Aug 28, 2023
1e8bbc6
Embed sirius inpto cp2k generator.
yakutovicha Aug 28, 2023
3d28258
Remove redundant sirius workchain.
yakutovicha Aug 28, 2023
cf4dbfd
Merge branch 'master' into master
yakutovicha Aug 28, 2023
4112b58
Fix minor issues, bump cp2k version.
yakutovicha Aug 29, 2023
72faf02
Remove generator_sirius.py
yakutovicha Aug 29, 2023
043c61b
Merge branch 'master' into master
yakutovicha Aug 29, 2023
a807603
Fix pre-commit.
yakutovicha Aug 29, 2023
e325cca
Rename sirius protocol to verification-pbe-v1-sirius
yakutovicha Aug 29, 2023
94f228a
Do not modify magnetic calculation parameters for sirius calculations.
yakutovicha Aug 30, 2023
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86 changes: 52 additions & 34 deletions aiida_common_workflows/workflows/relax/cp2k/generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,21 +38,25 @@ def dict_merge(dct, merge_dct):
dct[k] = merge_dct[k]


def get_kinds_section(structure: StructureData, basis_pseudo: str, magnetization_tags=None):
""" Write the &KIND sections given the structure and the settings_dict"""
def get_kinds_section(structure: StructureData, basis_pseudo=None, magnetization_tags=None, use_sirius=False):
"""Write the &KIND sections given the structure and the settings_dict."""
kinds = []
with open(pathlib.Path(__file__).parent / basis_pseudo, 'rb') as fhandle:
atom_data = yaml.safe_load(fhandle)
if basis_pseudo:
with open(pathlib.Path(__file__).parent / basis_pseudo, 'rb') as fhandle:
atom_data = yaml.safe_load(fhandle)
ase_structure = structure.get_ase()
symbol_tag = {
(symbol, str(tag)) for symbol, tag in zip(ase_structure.get_chemical_symbols(), ase_structure.get_tags())
}
for symbol, tag in symbol_tag:
new_atom = {
'_': symbol if tag == '0' else symbol + tag,
'BASIS_SET': atom_data['basis_set'][symbol],
'POTENTIAL': atom_data['pseudopotential'][symbol],
}
if use_sirius:
new_atom['POTENTIAL'] = f'UPF {symbol}.json'
else:
new_atom['BASIS_SET'] = atom_data['basis_set'][symbol]
new_atom['POTENTIAL'] = atom_data['pseudopotential'][symbol]
if magnetization_tags:
new_atom['MAGNETIZATION'] = magnetization_tags[tag]
kinds.append(new_atom)
Expand Down Expand Up @@ -125,6 +129,11 @@ def get_file_section():
'potential': potential,
}

def get_upf_pseudos_section(structure: StructureData, pseudo_family):
"""Provide the pseudos section to the input."""
pseudos_group = orm.load_group(pseudo_family)
return pseudos_group.get_pseudos(structure=structure)


class Cp2kCommonRelaxInputGenerator(CommonRelaxInputGenerator):
"""Input generator for the `Cp2kRelaxWorkChain`."""
Expand All @@ -150,7 +159,7 @@ def define(cls, spec):
super().define(spec)
spec.input(
'protocol',
valid_type=ChoiceType(('fast', 'moderate', 'precise', 'verification-pbe-v1')),
valid_type=ChoiceType(('fast', 'moderate', 'precise', 'verification-pbe-v1', 'sirius')),
default='moderate',
help='The protocol to use for the automated input generation. This value indicates the level of precision '
'of the results and computational cost that the input parameters will be selected for.',
Expand Down Expand Up @@ -190,36 +199,39 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
kpoints_distance = protocol_dict.pop('kpoints_distance', None)
kpoints = self._get_kpoints(kpoints_distance, structure, reference_workchain)
mesh, _ = kpoints.get_kpoints_mesh()
if mesh != [1, 1, 1]:
if 'sirius' in protocol:
parameters['FORCE_EVAL']['PW_DFT']['PARAMETERS']['NGRIDK'] = f'{mesh[0]} {mesh[1]} {mesh[2]}'
elif mesh != [1, 1, 1]:
builder.cp2k.kpoints = kpoints

magnetization_tags = None

# Metal or insulator.
# If metal then add smearing, unoccupied orbitals, and employ diagonalization.
if electronic_type == ElectronicType.METAL:
parameters['FORCE_EVAL']['DFT']['SCF']['SMEAR'] = {
'_': 'ON',
'METHOD': 'FERMI_DIRAC',
'ELECTRONIC_TEMPERATURE': '[K] 710.5',
}
parameters['FORCE_EVAL']['DFT']['SCF']['DIAGONALIZATION'] = {
'EPS_ADAPT': '1',
}
parameters['FORCE_EVAL']['DFT']['SCF']['MIXING'] = {
'METHOD': 'BROYDEN_MIXING',
'ALPHA': '0.1',
'BETA': '1.5',
}
parameters['FORCE_EVAL']['DFT']['SCF']['ADDED_MOS'] = 20
parameters['FORCE_EVAL']['DFT']['SCF']['CHOLESKY'] = 'OFF'

# If insulator then employ OT.
elif electronic_type == ElectronicType.INSULATOR:
parameters['FORCE_EVAL']['DFT']['SCF']['OT'] = {
'PRECONDITIONER': 'FULL_SINGLE_INVERSE',
'MINIMIZER': 'CG',
}
if 'sirius' in protocol:
# If metal then add smearing, unoccupied orbitals, and employ diagonalization.
if electronic_type == ElectronicType.METAL:
parameters['FORCE_EVAL']['DFT']['SCF']['SMEAR'] = {
'_': 'ON',
'METHOD': 'FERMI_DIRAC',
'ELECTRONIC_TEMPERATURE': '[K] 710.5',
}
parameters['FORCE_EVAL']['DFT']['SCF']['DIAGONALIZATION'] = {
'EPS_ADAPT': '1',
}
parameters['FORCE_EVAL']['DFT']['SCF']['MIXING'] = {
'METHOD': 'BROYDEN_MIXING',
'ALPHA': '0.1',
'BETA': '1.5',
}
parameters['FORCE_EVAL']['DFT']['SCF']['ADDED_MOS'] = 20
parameters['FORCE_EVAL']['DFT']['SCF']['CHOLESKY'] = 'OFF'

# If insulator then employ OT.
elif electronic_type == ElectronicType.INSULATOR:
parameters['FORCE_EVAL']['DFT']['SCF']['OT'] = {
'PRECONDITIONER': 'FULL_SINGLE_INVERSE',
'MINIMIZER': 'CG',
}

# Magnetic calculation.
if spin_type == SpinType.NONE:
Expand All @@ -235,7 +247,10 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:

# Starting magnetization.
basis_pseudo = protocol_dict.pop('basis_pseudo')
dict_merge(parameters, get_kinds_section(structure, basis_pseudo, magnetization_tags))
if 'sirius' in protocol:
dict_merge(parameters, get_kinds_section(structure, basis_pseudo=None, magnetization_tags=magnetization_tags, use_sirius=True))
else:
dict_merge(parameters, get_kinds_section(structure, basis_pseudo=basis_pseudo, magnetization_tags=magnetization_tags, use_sirius=True))

# Relaxation type.
if relax_type == RelaxType.POSITIONS:
Expand Down Expand Up @@ -281,7 +296,10 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
builder.handler_overrides = orm.Dict(dict={'restart_incomplete_calculation': True})

# Files.
builder.cp2k.file = get_file_section()
if 'sirius' in protocol:
builder.cp2k.pseudos_upf = get_upf_pseudos_section(structure, basis_pseudo)
else:
builder.cp2k.file = get_file_section()

# Input structure.
builder.cp2k.structure = structure
Expand Down
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